By tradition, all Freescale microcontrollers have all I/O pins set as unprotected inputs out of reset. I'm guessing the reason was power consumption, at some point in history. But whenever you speak to a Freescale technician, the always make the recommendation that set unused pins as outputs to make them safe. So there are two contradicting Freescale design advices: the shipped MCU comes with one default recommendation, the humans tell you another thing.
First of all, no pin should be left unconnected! Fix that first.
If the unused pins are left as inputs, there is a potential for circuit damage through transients and ESD. Every pin is internally protected with diodes, and some pins may also have pull resistors enabled out of reset. In my experience from using HCS08 and HCS12 during the past 10 years, these diodes are quite sufficient to handle various transients and EMC glitches, but they may not be able to handle ESD.
For safety-critical applications, I have used some simple, external protection on all I/O pins that are set as inputs out of reset, such as a pull-down resistor of 10k on unused pins. Some ports may have internal pull resistors enabled out of reset and then the external resistor isn't needed. Over the years, I have gradually started to replace these with the pin tied directly to ground, without any problems, so the external pull resistor might be a bit overkill. A lot will of course depend on the ground layout of the PCB.
All unused pins should be set as outputs through its DDR register. Set all unused port data register to zero (though they should already be zero out of reset). When the pin is set as output, it should be safe from most external signals, unless they are of an extreme nature. But note that since you set pins as outputs through software after MCU reset, any external voltages applied to the pin when the MCU program is not up and running, will be dangerous. You need external protection against that.
Overall, the main reason to pick Freescale MCUs is because they excellent at handling EMC and transients. The MCUs perform very well even in extreme environments. Personally, this is the one single reason I am using them.